Biochem Exam 3 Study Guide

Hydrogen bond

A weak bond that occurs when a hydrogen atom covalently bonded to an electronegative atom is attracted to another electronegative atom.

Van der Waals forces

Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Amino acids

Organic compounds that serve as the building blocks of proteins, classified based on their side chains.

Primary structure of proteins

The sequence of amino acids that make up a polypeptide chain.

Secondary structure of proteins

The local folded structures that form within a polypeptide due to interactions between non-adjacent amino acids, commonly alpha-helices and beta-pleated sheets.

Tertiary structure of proteins

The overall 3D shape of a polypeptide, determined by interactions among the amino acids.

Quaternary structure of proteins

The structure formed when two or more polypeptide chains assemble into a functional protein.

Enzymes

Biological catalysts that speed up biochemical reactions without being consumed.

Michaelis-Menten Kinetics

A model that describes the rate of enzyme-catalyzed reactions as a function of substrate concentration.

Lineweaver-Burk plot

A double reciprocal plot used to illustrate the Michaelis-Menten equation and determine enzyme kinetics.

Purines

Nitrogenous bases consisting of two fused rings; includes adenine (A) and guanine (G).

Pyrimidines

Nitrogenous bases consisting of a single ring; includes cytosine (C), thymine (T), and uracil (U).

Start codon

A specific codon (AUG) that signals the start of translation.

Stop codons

Codons (UAA, UAG, UGA) that signal the termination of translation.

DNA polymerase

An enzyme that synthesizes DNA by adding nucleotides to a growing chain.

RNA polymerase

An enzyme that synthesizes RNA from a DNA template.

Exonuclease activity

The activity of an enzyme that removes nucleotides from the ends of a DNA or RNA strand.

Promoter

A DNA sequence that signals the start site for transcription, where RNA polymerase binds.

Restriction enzymes

Proteins that cut DNA at specific sequences, enabling cloning.

Glycoproteins

Proteins that have carbohydrate groups attached, playing roles in cell signaling and recognition.

Saturated fatty acids

Fatty acids with no double bonds between carbon atoms, solid at room temperature.

Unsaturated fatty acids

Fatty acids with one or more double bonds, liquid at room temperature.

Hydropathy plots

Graphs created to predict the transmembrane segments of proteins based on their hydrophobic characteristics.

Integral membrane proteins

Proteins that are permanently attached to the cell membrane and can span the membrane.

Peripheral membrane proteins

Proteins that are temporarily attached to the membrane, often involved in signaling.

Passive transport

The movement of molecules across a cell membrane without the use of energy.

Active transport

The movement of molecules against their concentration gradient, requiring energy (ATP).

• primary active transporters: use ATP hydrolysis

• secondary active transporters: couple solute transport w/ ion

Na⁺/K⁺ ATPase

An enzyme that pumps sodium out of cells and potassium into cells, essential for maintaining membrane potential.

Transcription

The process of copying a segment of DNA into RNA.

Translation

The process of synthesizing proteins from messenger RNA.

Electrophysiology

The study of the electrical properties of biological cells and tissues.

adenine

guanine

thymine

cytosine

uracil

hairpin

a secondary structure of RNA where a single strand folds back on itself to form complementary base pairs, creating a loop-like configuration.

silent mutation

a type of mutation that does not change the amino acid sequence of the protein

missense mutation

a type of point mutation where one nucleotide base pair in the sequence is changed, resulting in the insertion of a different amino acid into the corresponding protein

nonsense mutation

a type of mutation that occurs when a nucleotide substitution changes an amino acid codon into a stop codon

frameshift mutation

a type of mutation where one or more nucleotides are inserted or deleted, resulting in a shift in the reading frame

southern blot method

a laboratory technique used to detect specific DNA sequences in DNA samples, involving the transfer of DNA from a gel to a membrane and hybridization with labeled probes.

DNA Synthesis

• reaction requires all 4 activated precursors: deoxynucleotide 5’-triphosphates (dNTPs) and Mg⁺²

• DNA polymerase requires a primer to begin

• elongation occurs in the 5’ to 3’ direction

nucleic acid hybridization method

synthetic bio method that uses the southern blot method to probe DNA genes

restriction enzymes

synthetic bio method using sequence specific DNAses, proteins that bind and cleave palindromic sequences

• restriction enzyme cuts genomic SNA, giving a specific set of DNA fragments of varying lengths

• fragments can be separated and visualised by agarose gel electrophoresis

• gives a “DNA fingerprint”

DNA Sequencing

synthetic bio method reaction that involves nucleophilic attack of 3’ OH of a DNA primer on a normal substrate (2’d NTP)

polymerase chain reaction (PCR)

synthetic bio method that amplifies a gene from a genome, requires DNAP, dsDNA (template), 2 DNA primers, and 4 dNTPs, involves a thermal cycle of 3 steps, repeated multiple times

Gene Cloning

1. amplify a gene from a human genome using PCR (include EcoRI sequence in primers)

2. cut w/ EcoRI: PCR product and plasmid (pSC101)

3. anneal DNA fragments and join w/ DNA ligase

requirements for expressing a cloned gene in E. Coli

1. gene must include a complete ORF

2. gene is often inserted into a polylinker of a plasmid; includes DNA replication origin, antibio resistance gene and sometimes a reporter gene

3. additional transcriptional and translational sequences are also needed: promotor & terminator, shine-dalgarno sequence

site-directed mutagenesis

synthetic bio method that uses a synthetic primer containing a mismatched nucleotide, this primer was annealed w/ a template strand containing a gene to be mutated

gene knockouts

genes can be replaced in a genome via homologous recombination, this method takes advantage of DNA repair enzymes

genome editing

genes can be mutated via double-stranded DNA breaks, this method is known by the acronym CRISPR

orthologs

homologs present within different species and have very similar/identical functions

paralog

homologs present within one species

homolog

homologous molecules

sequence alignments

used to determine whether two molecules are ortho/paralogs, aligned primary sequences can be used to predict 3D structures of related proteins, comparisons can be used to construct evolutionary trees

ab initio method

relies on computer modeling of protein folding, calculating non-covalent interaction energies (assuming that free energy of the folded protein is minimized

homology modeling methods

newer methods where proteins of unknown structure are first aligned with homologous proteins of known structure, differential interactions are predicted and refined, assuming correlated mutations or covariations

newest approaches in synthetic bio

AI-based modeling software such as AlphaFold and RoseTTAFold

designed proteins

new protein folds have been the cornerstone of de novo design to engineer new enzymes and other functional proteins

ex: enzymes to break down plastics, protein scaffolds to build new drug molecules

glycoproteins

a protein covalently attached to a carbohydrate group, extracellular proteins that regulate cell-cell interactions

N-linked (side chain of Asn) or O-linked (side chain of Ser or Thr)

monosaccharide

the simplest carbohydrate, contains a single aldehyde or ketone that has two or more hydroxyl groups, most have D configurations

ex: glucose, ribose, deoxyribose, mannose, galactose, fructose

disaccharide

composed of two monosaccharides, ex: sucrose, lactose, maltose

polysaccharide

composed of many monosaccharides, ex: cellulose, glycogen, amylose (starch), chitin

formation of a disaccharide

condensation forms a disaccharide, hydrolysis breaks one down

lectins and selectins

glycoproteins important for development in multicellular animals

proteoglycans

A protein containing one or more covalently linked glycosaminoglycan chains.

collagen

Cartilage proteoglycan, contains keratan sulfate and chondroitin chains linked to a polypeptide backbone. breakdown/lack of this causes arthritis

mucins (mucoproteins)

One of a class of glycoproteins, consisting mainly of carbohydrate, in which the protein component is extensively glycosylated to serine or threonine by N-acetylgalactosamine.

common features of biological membranes

1. Sheetlike structures (two molecules thick, 60Å to 100Å).

2. Lipid bilayers with both hydrophobic and hydrophilic components.

3. Proteins serve as pumps, channels, receptors, energy transducers, and enzymes.

4. Asymmetric with distinct inner and outer surfaces.

5. Fluid structures; 'lipids and proteins diffuse rapidly in the plane of the membrane. They do not readily rotate across the membrane.

6. Most cell membranes are electrically polarized (inside negative, -60 mV). Membrane potential is key for transport, energy conversion, and excitability.

general structure of fatty acids

three major kinds of lipids

phospholipids, glycolipids, and cholesterol

protein mediation in membranes

1. transport of molecules and ions (channels and pumps)

2. response to extracellular signals (receptors for hormones and light)

3. conduction of electrical currents (along the axons of nerve cells)

integral membrane proteins

(A, B, & D)

interact extensively with the hydrocarbon chains of membrane lipids, and they can be released only by agents that compete for these nonpolar interactions.

peripheral membrane proteins

(C)

bound to membranes primarily by electrostatic and hydrogen-bond interactions with the head groups of lipids. Many are bound to the surfaces of integral proteins, on either the cytoplasmic or the extracellular side of the membrane. Others are anchored to the lipid bilayer by a covalently attached hydrophobic chain, such as a fatty acid.

membrane-spanning alpha helices

the most common structural motif in membrane proteins, span the hydrophobic part

allows proteins to interact with the membrane

three transporters in conduction of nerve impulses

1. Na+/K+ ATPase

2. Na+ channel

3. K+ channel

selectivity filter

the narrowest diameter of the channel matches the size of a single K+ ion